4.7 Article

The fine-scale recombination rate variation and associations with genomic features in a butterfly

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)

L. Hook et al.

Summary: Karyotypes are usually similar between closely related species in the order Lepidoptera, but the extent of genome reshuffling in the wood white species complex is unknown. By analyzing the genomes of wood white species, it was discovered that there were extensive rearrangements, including comparisons between different Leptidea species. The results reveal that chromosome count alone may hide the true extent of genome restructuring and suggest that the genome evolution in Lepidoptera might be underestimated.

CHROMOSOME RESEARCH (2023)

Article Genetics & Heredity

Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus

Tobias Baril et al.

Summary: This study provides a detailed TE annotation and analysis for the monarch butterfly genome, revealing a lower TE content compared to other related species, but with some novel TE families rapidly expanding. The research also identifies associations between TEs and wing coloration and immune genes.

MOBILE DNA (2022)

Article Biology

Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map

Olli-Pekka Smolander et al.

Summary: Researchers provide a chromosome-level assembly of the Glanville fritillary butterfly genome from Pacific Biosciences sequencing of a pool of males, which is a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies.

GIGASCIENCE (2022)

Article Evolutionary Biology

High-Resolution Estimates of Crossover and Noncrossover Recombination from a Captive Baboon Colony

Jeffrey D. Wall et al.

Summary: This study investigates crossover and noncrossover recombination in olive baboons and compares the results to linkage disequilibrium-based recombination estimates. The study finds gender differences in recombination rates and a bimodal distribution of noncrossover tract lengths. Additionally, the study demonstrates the use of crossover and linkage disequilibrium-based recombination estimates in identifying genome assembly errors.

GENOME BIOLOGY AND EVOLUTION (2022)

Article Biotechnology & Applied Microbiology

Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly

Daria Shipilina et al.

Summary: The study identified gene family expansions and recombination patterns in the painted lady butterfly genome, revealing mechanisms of environmental adaptation. Lineage-specific gene family expansions were found to be associated with protein, fat metabolism, detoxification, and defense against infection. Recombination maps showed the impact of chromosome size on the recombination rate and a positive association between recombination and short interspersed elements.

GENOMICS (2022)

Article Evolutionary Biology

The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes

Jesper Boman et al.

Summary: Recombination reshuffles alleles through crossover and gene conversion, impacting genetic diversity. In wood white butterflies, gBGC is not the main determinant of genetic diversity; high linked selection and GC content reduce diversity. The joint effects of gBGC and mutation bias may resemble linked selection's impact on diversity levels.

GENOME BIOLOGY AND EVOLUTION (2021)

Article Biochemical Research Methods

Sensitive protein alignments at tree-of-life scale using DIAMOND

Benjamin Buchfink et al.

Summary: We are at the beginning of a genomic revolution where all known species are planned to be sequenced. The improved version of DIAMOND allows for quick tree-of-life scale protein alignments.

NATURE METHODS (2021)

Article Ecology

Prolonged diapause has sex-specific fertility and fitness costs

Aigi Margus et al.

EVOLUTIONARY ECOLOGY (2020)

Article Biochemistry & Molecular Biology

Natural Selection Shapes Variation in Genome-wide Recombination Rate in Drosophila pseudoobscura

Kieran Samuk et al.

CURRENT BIOLOGY (2020)

Review Genetics & Heredity

New Solutions to Old Problems: Molecular Mechanisms of Meiotic Crossover Control

Gerald R. Smith et al.

TRENDS IN GENETICS (2020)

Review Genetics & Heredity

From molecules to populations: appreciating and estimating recombination rate variation

Joshua V. Penalba et al.

NATURE REVIEWS GENETICS (2020)

Article Biochemistry & Molecular Biology

Recombination rate variation shapes barriers to introgression across butterfly genomes

Simon H. Martin et al.

PLOS BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Extreme Differences in Recombination Rate between the Genomes of a Solitary and a Social Bee

Julia C. Jones et al.

MOLECULAR BIOLOGY AND EVOLUTION (2019)

Article Biochemistry & Molecular Biology

Lack of gene flow: Narrow and dispersed differentiation islands in a triplet of Leptidea butterfly species

Venkat Talla et al.

MOLECULAR ECOLOGY (2019)

Article Genetics & Heredity

Crossover Interference: Shedding Light on the Evolution of Recombination

Sarah P. Otto et al.

Annual Review of Genetics (2019)

Article Biology

The impact of poly-A microsatellite heterologies in meiotic recombination

Angelika Heissl et al.

LIFE SCIENCE ALLIANCE (2019)

Article Multidisciplinary Sciences

GC content elevates mutation and recombination rates in the yeast Saccharomyces cerevisiae

Denis A. Kiktev et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Multidisciplinary Sciences

Versatility of multivalent orientation, inverted meiosis, and rescued fitness in holocentric chromosomal hybrids

Vladimir A. Lukhtanov et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Genetics & Heredity

Robust and scalable inference of population history froth hundreds of unphased whole genomes

Jonathan Terhorst et al.

NATURE GENETICS (2017)

Article Biochemistry & Molecular Biology

Direct determination of diploid genome sequences

Neil I. Weisenfeld et al.

GENOME RESEARCH (2017)

Article Biology

Connecting theory and data to understand recombination rate evolution

Amy L. Dapper et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2017)

Article Biology

Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies

Josep M. Comeron

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2017)

Review Biology

Variation in recombination frequency and distribution across eukaryotes: patterns and processes

Jessica Stapley et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2017)

Review Biology

Coevolution between transposable elements and recombination

Tyler V. Kent et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2017)

Review Genetics & Heredity

Control of Meiotic Crossovers: From Double-Strand Break Formation to Designation

Stephen Gray et al.

ANNUAL REVIEW OF GENETICS, VOL 50 (2016)

Article Biochemical Research Methods

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

Jerome Kelleher et al.

PLOS COMPUTATIONAL BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Neva C. Durand et al.

CELL SYSTEMS (2016)

Article Biochemistry & Molecular Biology

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

Neva C. Durand et al.

CELL SYSTEMS (2016)

Article Cell Biology

A novel role of farnesylation in targeting a mitotic checkpoint protein, human Spindly, to kinetochores

Devinderjit K. Moudgil et al.

JOURNAL OF CELL BIOLOGY (2015)

Article Plant Sciences

Meiotic recombination hotspots - a comparative view

Kyuha Choi et al.

PLANT JOURNAL (2015)

Article Multidisciplinary Sciences

Stable recombination hotspots in birds

Sonal Singhal et al.

SCIENCE (2015)

Article Genetics & Heredity

Repbase Update, a database of repetitive elements in eukaryotic genomes

Weidong Bao et al.

MOBILE DNA (2015)

Article Biochemistry & Molecular Biology

Estimation of the Spontaneous Mutation Rate in Heliconius melpomene

Peter D. Keightley et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Multidisciplinary Sciences

Repair of DNA double-strand breaks by templated nucleotide sequence insertions derived from distant regions of the genome

Masahiro Onozawa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Ecology

SHORT INDELS ARE SUBJECT TO INSERTION-BIASED GENE CONVERSION

Evgeny V. Leushkin et al.

EVOLUTION (2013)

Article Biochemistry & Molecular Biology

Meiotic Recombination Strongly Influences GC-Content Evolution in Short Regions in the Mouse Genome

Yves Clement et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Review Genetics & Heredity

Genomic signatures of selection at linked sites: unifying the disparity among species

Asher D. Cutter et al.

NATURE REVIEWS GENETICS (2013)

Article Genetics & Heredity

Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera

Christine A. Lavoie et al.

MOBILE DNA (2013)

Article Biochemistry & Molecular Biology

Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome

Erik Axelsson et al.

GENOME RESEARCH (2012)

Article Genetics & Heredity

The Many Landscapes of Recombination in Drosophila melanogaster

Josep M. Comeron et al.

PLOS GENETICS (2012)

Article Biochemical Research Methods

The variant call format and VCFtools

Petr Danecek et al.

BIOINFORMATICS (2011)

Review Ecology

Recombination rate variation in closely related species

C. S. Smukowski et al.

HEREDITY (2011)

Article Biodiversity Conservation

Evidence-based National Recovery Plan for Leptidea sinapis (wood white butterfly) in Southern Britain

Stephen Jeffcoate et al.

JOURNAL OF INSECT CONSERVATION (2011)

Article Biochemistry & Molecular Biology

Population Genomics of Transposable Elements in Drosophila melanogaster

Dmitri A. Petrov et al.

MOLECULAR BIOLOGY AND EVOLUTION (2011)

Article Biochemistry & Molecular Biology

GC-Biased Gene Conversion and Selection Affect GC Content in the Oryza Genus (rice)

Aline Muyle et al.

MOLECULAR BIOLOGY AND EVOLUTION (2011)

Article Multidisciplinary Sciences

Inference of human population history from individual whole-genome sequences

Heng Li et al.

NATURE (2011)

Article Multidisciplinary Sciences

Unexpected layers of cryptic diversity in wood white Leptidea butterflies

Vlad Dinca et al.

NATURE COMMUNICATIONS (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

The recombination landscape of the zebra finch Taeniopygia guttata genome

Niclas Backstrom et al.

GENOME RESEARCH (2010)

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Genetics & Heredity

THE KINETOCHORE AND THE BIVALENT STRUCTURE IN THE LEPIDOPTERA

ESKO SUOMALAINEN

HEREDITAS (2010)

Review Genetics & Heredity

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

Laurent Duret et al.

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS (2009)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Biotechnology & Applied Microbiology

Alu repeats increase local recombination rates

David J. Witherspoon et al.

BMC GENOMICS (2009)

Article Genetics & Heredity

Achiasmatic oogenesis in the Heliconiine butterflies

Esko Suomalainen et al.

HEREDITAS (2009)

Review Ecology

The evolution of restricted recombination in sex chromosomes

Roberta Bergero et al.

TRENDS IN ECOLOGY & EVOLUTION (2009)

Article Genetics & Heredity

Accelerated Evolution of the Prdm9 Speciation Gene across Diverse Metazoan Taxa

Peter L. Oliver et al.

PLOS GENETICS (2009)

Article Biotechnology & Applied Microbiology

High frequency of microsatellites in S. cerevisiae meiotic recombination hotspots

Andrew T. M. Bagshaw et al.

BMC GENOMICS (2008)

Article Genetics & Heredity

Meiotic recombination at the ends of chromosomes in Saccharomyces cerevisiae

Arnold B. Barton et al.

GENETICS (2008)

Article Genetics & Heredity

The Recombinational Anatomy of a Mouse Chromosome

Kenneth Paigen et al.

PLOS GENETICS (2008)

Review Genetics & Heredity

Opinion - Recombination: an underappreciated factor in the evolution of plant genomes

Brandon S. Gaut et al.

NATURE REVIEWS GENETICS (2007)

Article Biochemistry & Molecular Biology

Exceptionally high levels of recombination across the honey bee genome

Martin Beye et al.

GENOME RESEARCH (2006)

Article Biochemical Research Methods

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure

Adrian Alexa et al.

BIOINFORMATICS (2006)

Article Multidisciplinary Sciences

A fine-scale map of recombination rates and hotspots across the human genome

S Myers et al.

SCIENCE (2005)

Article Genetics & Heredity

A genetic linkage map of the mimetic butterfly Heliconius melpomene

CD Jiggins et al.

GENETICS (2005)

Article Multidisciplinary Sciences

The fine-scale structure of recombination rate variation in the human genome

GAT McVean et al.

SCIENCE (2004)

Article Biochemistry & Molecular Biology

Comparative recombination rates in the rat, mouse, and human genomes

MI Jensen-Seaman et al.

GENOME RESEARCH (2004)

Article Biochemistry & Molecular Biology

Recombination drives the evolution of GC-content in the human genome

J Meunier et al.

MOLECULAR BIOLOGY AND EVOLUTION (2004)

Article Biochemistry & Molecular Biology

Holocentric chromosomes in meiosis. I. Restriction of the number of chiasmata in bivalents

S Nokkala et al.

CHROMOSOME RESEARCH (2004)

Article Biochemistry & Molecular Biology

On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster

C Bartolomé et al.

MOLECULAR BIOLOGY AND EVOLUTION (2002)

Letter Biochemistry & Molecular Biology

Local rates of recombination are positively correlated with GC content in the human genome

SM Fullerton et al.

MOLECULAR BIOLOGY AND EVOLUTION (2001)

Article Multidisciplinary Sciences

Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes

G Marais et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)

Article Multidisciplinary Sciences

Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae

JL Gerton et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)

Article Biochemistry & Molecular Biology

Detection and distribution patterns of telomerase activity in insects

T Sasaki et al.

EUROPEAN JOURNAL OF BIOCHEMISTRY (2000)